BACKGROUND In 2022, an outbreak of mpox that started in European countries spread worldwide through human-to-human transmission. Cases have been mostly mild, but severe clinical presentations have been reported. In these cases, tecovirimat has been the drug of choice to treat patients with aggravated disease. OBJECTIVES Here we investigated the tecovirimat susceptibility of 18 clinical isolates of monkeypox virus (MPXV) obtained from different regions of Brazil. METHODS Different concentrations of tecovirimat were added to cell monolayers infected with each MPXV isolate. After 72 hours, cells were fixed and stained for plaque visualization, counting, and measurement. The ortholog of F13L gene from each MPXV isolate was polymerase chain reaction (PCR)-amplified, sequenced, and the predicted protein sequences were analyzed. FINDINGS The eighteen MPXV isolates generated plaques of different sizes. Although all isolates were highly sensitive to the drug, two showed different response curves and IC50 values. However, the target protein of tecovirimat, F13 (VP37), was 100% conserved in all MPXV isolates and therefore does not explain the difference in sensitivity. MAIN CONCLUSIONS Our results support screening different MPXV isolates for tecovirimat susceptibility as an important tool to better use of the restricted number of tecovirimat doses available in low-income countries to treat patients with mpox. 2022 humantohuman human transmission mild reported cases disease 1 (MPXV Brazil 7 hours visualization counting measurement FL F L PCRamplified, PCRamplified PCR amplified, amplified (PCR)-amplified sequenced analyzed sizes IC IC5 values However F1 VP37, VP37 VP , (VP37) 100 sensitivity lowincome low income 202 VP3 (VP37 10 20 (VP3 2 (VP

ABSTRACT The Severe Acute Respiratory Syndrome Coronavirus-2 (SARS-CoV-2) pandemic demanded rapid diagnosis to isolate new COVID-19 cases and prevent disease transmission. Quantitative Real-Time Polymerase Chain Reaction (qRT-PCR) rapidly became the gold standard for diagnosis. However, due to the high cost and delay of the results, other types of diagnosis were implemented, such as COVID-19 Ag Rapid Tests and Reverse Transcription Technique followed by Loop-Mediated isothermal Amplification (RT-LAMP). In this work, we validated the use of RT-LAMP in saliva samples rather than nasopharyngeal swabs, as the collection is more comfortable. First, we selected 5 primer sets based on the limit of detection for SARS-CoV-2 RNA, then validated their sensitivity and specificity in patient samples. A total of 117 samples were analyzed by fluorometric RT-LAMP and compared with qRT-PCR results. Our results show that the use of a high-sensitive primer ORF1-a, together with a low-sensitive primer set Gene E (time to threshold of 22.9 and 36.4 minutes, respectively, using 200 copies of viral RNA), achieved sensitivity in purified RNA from saliva samples of 95.2% (95% CI 76.1-99.8) with 90.5% specificity (95% CI 69.6-98.8) (n = 42).As RNA purification increases the turnaround time, we tested the outcome of RT-LAMP utilizing raw saliva samples without purification. The test achieved a sensitivity of 81.8% (95% CI 59.7-94.8) and a specificity of 90.9% (95% CI 70.8-98.8). As a result, the accuracy of 92.9% (95% CI 80.5-98.5) in purified RNA-saliva samples was lowered to an acceptable level of 86.4% (95% CI 72.6-94.8) in raw saliva. Although mass vaccination has been implemented, new strains and low vaccination progress helped to spread COVID-19. This study shows that it is feasible to track new COVID-19 cases in a large population with the use of raw saliva as sample in RT-LAMP assay which yields accurate results and offers a less invasive test. Coronavirus2 Coronavirus 2 Coronavirus- SARSCoV2 SARSCoV SARS CoV (SARS-CoV-2 COVID19 COVID 19 COVID-1 transmission RealTime Real Time qRTPCR qRT PCR (qRT-PCR However implemented LoopMediated Loop Mediated RTLAMP. RTLAMP RT LAMP . (RT-LAMP) work swabs comfortable First SARS-CoV- 11 highsensitive sensitive ORF1a, ORF1a ORFa ORF1 a, ORF ORF1-a lowsensitive time 229 22 9 22. 364 36 4 36. minutes respectively 20 , RNA) 952 95 95.2 95% (95 76.199.8 761998 76.1 99.8 76 1 99 8 76.1-99.8 905 90 90.5 69.698.8 696988 69.6 98.8 69 6 98 69.6-98.8 n 42.As 42As 42 .As 818 81 81.8 59.794.8 597948 59.7 94.8 59 7 94 59.7-94.8 909 90.9 70.898.8. 708988 70.8 70 70.8-98.8) result 929 92 92.9 80.598.5 805985 80.5 98.5 80 80.5-98.5 RNAsaliva 864 86 86.4 72.694.8 726948 72.6 72 72.6-94.8 COVID19. 19. (SARS-CoV- COVID1 COVID- (RT-LAMP SARS-CoV 3 95. (9 199 76.199. 76199 761 76. 998 99. 76.1-99. 90. 698 69.698. 69698 696 69. 988 98. 69.6-98. 81. 794 59.794. 59794 597 59. 948 94. 59.7-94. 898 70.898.8 70898 708 70. 70.8-98.8 92. 598 80.598. 80598 805 80. 985 80.5-98. 86. 694 72.694. 72694 726 72. 72.6-94. (SARS-CoV ( 76.199 7619 76.1-99 69.698 6969 69.6-98 79 59.794 5979 59.7-94 89 70.898. 7089 70.8-98. 80.598 8059 80.5-98 72.694 7269 72.6-94 76.19 76.1-9 69.69 69.6-9 59.79 59.7-9 70.898 70.8-98 80.59 80.5-9 72.69 72.6-9 76.1- 69.6- 59.7- 70.89 70.8-9 80.5- 72.6- 70.8-

Abstract Since the first reported case of COVID-19 in Brazil, the public and private educational system started to close. Up to November 2020, scientific discussions about the return of schooling activities have been rarely performed by the national scientific community and police-makers. The great delay of school returning in Brazil contrasts with successful international strategies of school reopening worldwide and seems counterintuitive with the reopening of non-essential activities. Here, important issues to be considered before and during school reopening are reviewed and discussed. COVID-19 testing is essential to avoid disease spreading, but high cost of individual RT-qPCRs impairs an extensive testing strategy for school returning. To reduce costs and increase the speed of diagnosis, we tested the efficiency of a pooled-sample PCR strategy in a cohort of the educational staff in the city of Macaé/RJ, finding five asymptomatic individuals (0,66%) among the 754 people tested. Thus, a polled-sample PCR testing strategy of the educational staff might prevent infection spreading in schools at a reasonable cost. We discuss how our test strategy could be coupled with internationally recognized safety rules to allow for a safe school return and how countries from different world regions are dealing with educational activities during COVID-19 pandemic.

ABSTRACT In response to the Zika epidemics in Brazil, the ZDC molecular assay (Bio-Manguinhos) was developed and registered at the Brazilian Regulatory Agency of Health Surveillance - ANVISA. The circulation of Zika (ZIKV) Dengue (DENV) and Chikungunya (CHIKV) viruses and their clinical similarities are challenges to correctly diagnose these viruses. The simultaneous detection of ZIKV, DENV and CHIKV is an important tool for diagnosis and surveillance. Here, we present the analytical and clinical performance evaluation of ZDC molecular assay (Bio-Manguinhos) at the public health laboratories three years after its registration at ANVISA. The clinical performance demonstrates the ZDC molecular assay (Bio-Manguinhos) has 100% sensitivity and 100% specificity to detect and discriminate ZIKV, CHIKV, and DENV from clinical plasma samples. The ZDC molecular assay (Bio-Manguinhos) results were highly reproducible and no cross-reactivity was seen during testing with a panel of other infectious agents. In conclusion, the ZDC molecular assay (Bio-Manguinhos) is an accurate and reliable tool to monitor Zika, dengue and chikungunya infections in countries like Brazil with simultaneous circulation of the three viruses.

BACKGROUND The high demand for adequate material for the gold standard reverse transcription real-time polymerase chain reaction (RT-qPCR)-based diagnosis imposed by the Coronavirus disease 2019 (COVID-19) pandemic, combined with the inherent contamination risks for healthcare workers during nasopharyngeal swab (NP) sample collection and the discomfort it causes patients, brought the need to identify alternative specimens suitable for the diagnosis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2). OBJECTIVES The aim of this work was to compare saliva and gingival fluid swabs to NP swabs as specimens for RT-qPCR-based SARS-CoV-2 diagnosis. METHODS We compared gingival fluid swabs (n = 158) and saliva (n = 207) to the rayon-tipped NP swabs obtained from mild-symptomatic and asymptomatic subjects as specimens for RT-qPCR for SARS-CoV-2 detection. FINDINGS When compared to NP swabs, gingival fluid swabs had a concordance rate of 15.4% among positive samples, zero among inconclusive, and 100% among negative ones. For saliva samples, the concordance rate was 67.6% among positive samples, 42.9% among inconclusive, and 96.8% among negative ones. However, the concordance rate between saliva and NP swabs was higher (96.9%) within samples with lower cycle threshold (Ct) values (Ct > 10 ≤ 25). MAIN CONCLUSIONS Our data suggests that whereas gingival fluid swabs are not substitutes for NP swabs, saliva might be considered whenever NP swabs are not available or recommended.

BACKGROUND During routine Coronavirus disease 2019 (COVID-19) diagnosis, an unusually high viral load was detected by reverse transcription real-time polymerase chain reaction (RT-qPCR) in a nasopharyngeal swab sample collected from a patient with respiratory and neurological symptoms who rapidly succumbed to the disease. Therefore we sought to characterise the infection. OBJECTIVES We aimed to determine and characterise the etiological agent responsible for the poor outcome. METHODS Classical virological methods, such as plaque assay and plaque reduction neutralisation test combined with amplicon-based sequencing, as well as a viral metagenomic approach, were performed to characterise the etiological agents of the infection. FINDINGS Plaque assay revealed two distinct plaque phenotypes, suggesting either the presence of two severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) strains or a productive coinfection of two different species of virus. Amplicon-based sequencing did not support the presence of any SARS-CoV-2 genetic variants that would explain the high viral load and suggested the presence of a single SARS-CoV-2 strain. Nonetheless, the viral metagenomic analysis revealed that Coronaviridae and Herpesviridae were the predominant virus families within the sample. This finding was confirmed by a plaque reduction neutralisation test and PCR. MAIN CONCLUSIONS We characterised a productive coinfection of SARS-CoV-2 and Herpes simplex virus 1 (HSV-1) in a patient with severe symptoms that succumbed to the disease. Although we cannot establish the causal relationship between the coinfection and the severity of the clinical case, this work serves as a warning for future studies focused on the interplay between SARS-CoV-2 and HSV-1 coinfection and COVID-19 severity.

ABSTRACT Introduction: In the current standard of care (SoC) RT-PCR method for COVID-19, the patient’s swab was extracted in viral transport media (VTM). For the PanbioTM COVID-19 Ag Rapid Test, the patient swab is flushed out in extraction buffer, of which a small fraction is used for testing, leaving more than half the sample unused. This study was designed to show that RT-PCR results from the residual sample of the PanbioTM COVID-19 Ag Rapid Test (called Novel RT-PCR) are not worse than the SoC RT-PCR result. Methods: The study was performed using (1) dilution series of five patient samples, and (2) 413 patient samples comparing SOC versus Novel RT-PCR results. Results: For the dilution series samples, all tested positive by both methods. The bias between Ct values of Novel RT-PCR and SoC RT-PCR did not exceed 3.00 Ct using primers N1 and N2. A total of 413 COVID symptomatic patients seeking COVID testing were tested, of which 89 patients tested positive and 324 tested negative with SoC RT-PCR. In 324 patients who tested negative with SoC RT-PCR, 323 tested negative with Novel RT-PCR, and one (1) tested positive. Out of 89 who tested positive with SoC RT-PCR, 80 tested positive with the Novel RT-PCR, and nine patients showed a negative test result. The Overall Percent Agreement for the 413 valid patient sample pairs was 97.5 [95% CI 97 to 98]. Conclusion: The study demonstrated that the performance of the Novel RT-PCR method is acceptable compared to the SoC RT-PCR method and can be a useful tool to perform RTPCR without the need for new swab collections.

Abstract INTRODUCTION Rio de Janeiro has hardly experienced coronavirus disease. METHODS Here, 87,442 reverse transcription polymerase chain reaction (RT-PCR) test results for severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) were reported among Rio de Janeiro residents (March to September 2020). RESULTS Overall, RT-PCR positivity of 44.6% decreased over time towards 20%. Positivity was greater among males (OR=1.22; 95%CI:1.19-1.26); Black (OR=1.10; 95%CI:1.02-1.19), Brown (OR=1.16; 95%CI:1.10-1.22), and indigenous people (OR=2.11; 95%CI:0.88-5.03) compared to Whites and increased with age; with epidemic spread from the capital to inland regions. CONCLUSIONS SARS-CoV-2 keeps spreading in Rio de Janeiro, and reopening of activities may fuel the epidemic.

ABSTRACT A new point-of-care HIV viral load, mPIMA HIV-1/2 VL, Abbott, USA, has been recently developed. This point-of-care viral load requires no skilled person to run and uses a small plasma volume (50 µL). However, obtaining 50 µL of plasma can be a challenge in limited resource settings. We validated a simple and easy method to obtain enough amount of plasma to run a point-of-care viral load. The study utilized 149 specimens from patients failing antiretroviral therapy. At least 250 µL of whole blood was collected in a microtube/EDTA from fingerstick (fs-plasma) and immediately centrifuged. Parallel collection of venous blood to obtain plasma (vp-plasma) was used to compare performance in a point-of-care viral load assay and in methodology used in centralized laboratories Abbott M2000, Abbott, USA. The procedure for plasma collection takes less than 10 min and in 94% of the cases only one fingerstick was sufficient to collect at least 250 µL of blood. The Pearson correlation coefficient value for vp-plasma versus fs-plasma ran on mPIMA was 0.990. The Bland-Altman mean difference (md) for this comparison were virtually zero (md = −0.001) with limits of agreement between −0.225 and 0.223. In addition, the Pearson correlation coefficient value for fs-plasma in mPIMA versus vp-plasma in Abbott M2000 was 0.948 for values above the mPIMA limit of quantification (LoQ; from 800 to 1,000,000 copies/mL). These results validate this simple plasma isolation method capable to be implemented in low resource countries where point-of-care decentralization is deeply needed.

Abstract Hepatitis C virus (HCV) infection is a worldwide health problem. Nowadays, direct-acting antiviral agents (DAAs) are the main treatment for HCV; however, the high level of virus variability leads to the development of resistance-associated variants (RAVs). Thus, assessing RAVs in infected patients is important for monitoring treatment efficacy. The aim of our study was to investigate the presence of naturally occurring resistance mutations in HCV NS3 and NS5 regions in treatment-naïve patients. Ninety-six anti-HCV positive serum samples from blood donors at the Center of Hematology and Hemotherapy of Santa Catarina State (HEMOSC) were collected retrospectively in 2013 and evaluated in this study. HCV 1a (37.9%), 1b (25.3%), and 3a (36.8%) subtypes were found. The frequency of patients with RAVs in our study was 6.9%. The HCV NS5b sequencing reveled 1 sample with L320F mutation and 4 samples with the C316N/R polymorphism. The analysis of the NS3 region revealed the D168A/G/T (3.45%), S122G (1.15%), and V55A (2.3%) mutations. All samples from genotype 3a (36.8%) presented the V170 I/V non-synonymous mutation. In conclusion, we have shown that mutations in NS3 and NS5b genes are present in Brazilian isolates from therapy-naïve HCV patients.

Abstract Recent reports indicate that besides respiratory and systemic symptoms among coronavirus disease (COVID-19) patients, the disease has a wide spectrum of neurological manifestations (encephalitis, meningitis, myelitis, acute disseminated encephalomyelitis, metabolic and acute hemorrhagic necrotizing encephalopathy, cerebrovascular diseases, Guillain-Barré syndrome, polyneuritis cranialis, dysautonomia, and myopathies). The severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) can spread from the respiratory system to the central nervous system, using transneuronal and hematogenous mechanisms. Although not every COVID-19 patient will test positive for the virus in the cerebrospinal fluid exam, the appearance of neurological symptoms associated with SARS-CoV-2 infection reveals the importance of understanding the neurologic manifestations and capacity for neural invasion associated with the pathogen. These aspects are relevant for correct diagnosis and treatment, and for the potential development of vaccines. This review highlights the latest evidence of SARS-CoV-2 infection with a focus on neurological involvement and potential neuropathogenesis mechanisms.

BACKGROUND Dengue is an arthropod-borne viral disease with a majority of asymptomatic individuals and clinical manifestations varying from mild fever to severe and potentially lethal forms. An increasing number of genetic studies have outlined the association between host genetic variations and dengue severity. Genes associated to viral recognition and entry, as well as those encoding mediators of the immune response against infection are strong candidates for association studies. OBJECTIVES The aim of this study was to investigate the association between MBL2, CLEC5A, ITGB3 and CCR5 genes and dengue severity in children. METHODS A matched case-control study was conducted and 19 single nucleotide polymorphisms (SNPs) were investigated. FINDINGS No associations were observed in single SNP analysis. However, when MBL2 SNPs were combined in haplotypes, the allele rs7095891G/rs1800450C/ rs1800451C/rs4935047A/rs930509G/rs2120131G/rs2099902C was significantly associated to risk of severe dengue under α = 0.05 (aOR = 4.02; p = 0.02). A second haplotype carrying rs4935047G and rs7095891G alleles was also associated to risk (aOR = 1.91; p = 0.04). MAIN CONCLUSIONS This is the first study to demonstrate the association between MBL2 haplotypes and dengue severity in Brazilians including adjustment for genetic ancestry. These results reinforce the role of mannose binding lectin in immune response to DENV.

RESUMO Introdução: As infecções sexualmente transmissíveis (ISTs) ainda são um importante problema de saúde pública, e a vigilância é essencial para sua prevenção e seu controle. Objetivo: Avaliar a prevalência das ISTs em uma unidade de referência ginecológica no Rio de Janeiro, Brasil. Materiais e métodos: Trata-se de um estudo transversal realizado entre agosto de 2016 e junho de 2017. Foram coletados sangue total e células cervicais de 62 mulheres e realizados testes para detecção de papiloma vírus humano (HPV), vírus da imunodeficiência humana (HIV), sífilis, clamídia, gonorreia e vírus do herpes simples 1 e 2 (HSV-1/2). As lesões cervicais foram diagnosticadas por citopatologia, e em algumas pacientes, por colposcopia (79%). Outras ISTs foram avaliadas durante o exame clínico. Resultados: Foram encontradas lesões cervicais pelo exame citopatológico em 46,8% das pacientes; aquelas com história de quatro parceiros sexuais tiveram mais risco de desenvolvê-las. Houve concordância moderada entre os resultados da citopatologia e colposcopia (Kappa = 0,69). A prevalência de HSV (96,7%), sífilis (6,4%) e HIV (3,2%) foi maior que a descrita na literatura, enquanto a prevalência de clamídia (6,4%) e gonorreia (1,6%) foi similar. O HPV foi detectado em 53,2% das mulheres, sendo 32,3% delas infectadas pelo HPV 16. No contexto das coinfecções, 38 mulheres (61,3%) tinham mais de uma IST. Conclusão: Visto que a maioria das mulheres analisadas era acometida por mais de uma IST, nossos resultados sugerem que uma triagem rotineira dessas infecções nas unidades de saúde poderia auxiliar na detecção precoce, bem como no tratamento e na prevenção. Essas medidas também impactariam no controle do câncer cervical das pacientes.

ABSTRACT Introduction: Sexually transmitted infections (STI) remain a major public health problem and surveillance is crucial for prevention and control strategies. Objective: Our aim was to assess the prevalence of STI in a reference center for gynecology in Rio de Janeiro, Brazil. Materials and methods: It is a cross-sectional study conducted between August 2016 and June 2017. Whole blood and cervical cells were collected from 62 women and tested for human papillomavirus (HPV), human immunodeficiency virus (HIV), syphilis, chlamydia, gonorrhea and herpes simples virus 1 and 2 (HSV-1/2). Cervical lesions were diagnosed by cytopathology and in some patients by colposcopy (79%). Other STI were evaluated during clinical examination. Results: Cervical lesions were detected by cytopathology examinations in 46.8% of patients; those with a history of four sexual partners were at higher risk of developing them. There was moderate agreement between the cytopathology e colposcopy results (Kappa = 0.69). The prevalence of HSV (96.7%), syphilis (6.4%) and HIV (3.2%) were higher than that described in the literature, while the prevalence of chlamydia (6.4%) and gonorrhea (1.6%) were similar. HPV was detected in 53.2% of women, 32.3% of which were infected by HPV 16. In the context of co-infections, 38 women (61.3%) presented more than one STI. Conclusion: Since most of the women analyzed were affected by more than one STI, our results suggest that routine screening for these infections at health centers would help in early detection, treatment and prevention of these infections. These measures would also impact on patients’ cervical cancer control.

ABSTRACT The Brazilian Public Health Service provides freely αPEG-IFN to treat patients infected with HCV. The primary goal of HCV therapy is the long-term elimination of HCV from the blood to reduce the risk of HCV associated complications and death. Patient viremia affects the treatment duration and response, thus influencing clinical decisions. We developed a high-throughput method to perform the quantification of RNA hepatitis C virus (HCV) virus load in plasma samples to monitor patients under treatment. The method is based on a duplex detection, in a one-step real-time RT-PCR assay and it has been validated according to the rules established by the official Brazilian regulatory agency (ANVISA). This new method was compared to a commercial kit (Cobas/Taqman HCV Test v2.0 - Roche), showing virus load results with significant correlation between them (p= 0,012) using commercial and clinical panels. In addition, 611 samples from patients treated with peguilated alfa-interferon (αPEG-IFN) from different regions of Brazil were analyzed. Our one-step real-time RT-PCR assay demonstrated good performance in viral load measurement and in treatment course monitoring, with acceptable sensitivity and specificity values.